Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.

ggmsa(
msa,
start = NULL,
end = NULL,
font = "helvetical",
color = "Chemistry_AA",
custom_color = NULL,
char_width = 0.9,
none_bg = FALSE,
by_conservation = FALSE,
posHighligthed = NULL,
seq_name = NULL,
border = NULL,
consensus_views = FALSE,
use_dot = FALSE,
disagreement = TRUE,
ignore_gaps = FALSE,
ref = NULL,
show.legend = FALSE
)

Arguments

msa Multiple aligned sequence files or objects representing either nucleotide sequences or AA sequences. a numeric vector. Start position to plot. a numeric vector. End position to plot. font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. If font = NULL, only plot the background tile. a Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER', 'CN6', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'. A data frame with two cloumn called "names" and "color".Customize the color scheme. a numeric vector. Specifying the character width in the range of 0 to 1. Defaults is 0.9. a logical value indicating whether background should be disaplayed. Defaults is FALSE. a logical value. The most conserved regions have the brightest colors. A numeric vector of the position that need to be highlighted. a logical value indicating whether seqence names should be displayed. Defaults is 'NULL' which indicates that the sequence name is displayed when 'font = null', but 'font = char' will not be displayed. If 'seq_name = TRUE' the sequence name will be displayed in any case. If 'seq_name = FALSE' the sequence name will not be displayed under any circumstances. a character string. The border color. a logical value that opeaning consensus views. a logical value. Displays characters as dots instead of fading their color in the consensus view. a logical value. Displays characters that disagreememt to consensus(excludes ambiguous disagreements). a logical value. When selected TRUE, gaps in column are treated as if that row didn't exist. a character string. Specifying the reference sequence which should be one of input sequences when 'consensus_views' is TRUE. logical. Should this layer be included in the legends?

ggplot object

Guangchuang Yu

Examples

#plot multiple sequences by loading fasta format
fasta <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(fasta, 164, 213, color="Chemistry_AA")

#XMultipleAlignment objects can be used as input in the 'ggmsa'